Hey everyone,
I was playing around with @chauffeur_afni to create images and I noticed that for axial and coronal views in montages, the image is flipped such that left = right. I confirmed this by manually loading the dataset into AFNI and checking it out using the normal viewing windows. Attached are 2 images. The first is the montage output from @chauffeur_afni where I want you to focus on the pattern of activation in the last image on the bottom right. Then, the next image is a screenshot from AFNI showing clearly that the image in the @chauffeur_afni montage matches this left = right view. What's weird is that this problem occurs in the axial and coronal views output from @chauffeur_afni but the sagittal view is fine (i.e., left = left for that one).
Finally, here is my @chauffeur_afni code whereby I specify that left should be left:
# Finally, create montage for correlation images
# Set top directory and go to it
set topdir_corr = /mnt/c/Users/brrobert/OneDriveUW/Desktop/fMRIdata/Correlation_Files
cd topdir_corr
# Set contrast label and brick numbers
set contrast_label = DW
set mean_brick_number = 4
set tstat_brick_number = 5
set min_cluster = 20
# Create new results output directory to store all of the correlation results in
set outputdir = ${topdir_corr}/${contrast_label}_Correlation_Images
if ( ! -d $outputdir ) mkdir $outputdir
# Create overlay montage image sets for this contrast
@chauffeur_afni \
-ulay TT_N27+tlrc \
-olay Correlations_DW+tlrc \
-cbar Reds_and_Blues_Inv \
-pbar_saveim ${outputdir}/Reds_and_Blues_Inv_Colour_Bar.jpg \
-pbar_dim 128x1022 \
-clusterize "-NN 2 -bisided p=0.001 -clust_nvox ${min_cluster} -orient LPI" \
-set_subbricks -1 "SpmnCorr#0" "SpmnCorr#0" \
-thr_olay_p2stat 0.01 \
-thr_olay_pside bisided \
-olay_alpha Yes \
-olay_boxed Yes \
-opacity 9 \
-prefix ${outputdir}/${contrast_label}_Clust_Montage2 \
-montx 5 -monty 2 -montgap 0 \
-set_xhairs OFF \
-label_mode 1 -label_size 4 -label_color white -label_setback 0.01 -label_string "" \
-box_focus_slices group_mask_.7olap+tlrc. \
-save_ftype PNG \
-blowup 4 \
-left_is_left LIL \
-do_clean